Support is requested for a conference MODELING OF PROTEIN INTERACTIONS IN GENOMES. The conference will be held at the Lightsey Conference Center in Charleston, SC, on June 16-19, 2001, and will focus on the computational procedures for reconstruction and study of the network of connections between proteins in genomes. The networks of connections between proteins have to be built by a combination of experimental studies, knowledge-based methods, sequence analysis, and structural approaches. The goal of this conference is to discuss realistic aims, computational methods development, and applications. The following topics will be covered: protein-protein docking (structure prediction and binding simulation), energetics of protein-protein association (energy landscapes, stability of complexes), protein structure-function relationships (functional assignment of protein structures, binding site prediction), interacting and noninteracting proteins (structure-based and sequence-based approaches, pathways, experimental approaches), modulating protein-protein interactions by small ligands, and the design of small molecules that can play some roles of native proteins in specific interactions. The conference will be relatively small, with approximately 100 participants. The invited speakers will represent the protein docking community, including Michael Sternberg, ICRF, UK; Joel Janin, CNRS, France; and Ruth Nussinov, NIH, as well as researchers working on the energetics and kinetics of protein-protein association; e.g., Barry Honig, Columbia University; Andrew McCammon, UCSD; Harold Scheraga, Cornell University; and Peter Wolynes, UCSD. The relationship between protein structure and function will be addressed (Jeffrey Skolnick, Danforth Center; and Adam Godzik, Burnham Institute). An entire section will be devoted to the modulation of protein-protein interactions by small molecules (e.g., Arthur Olson, Scripps Institute; Brian Shoichet, Northwestern University, and researchers from the pharmaceutical indutry), and another to the experimental analysis of protein-protein interactions, including two-hybrid studies and the identification of pathways, including the current state of pathway libraries. A poster session will be held on one of the conference days.